generated from opensafely/research-template
/
project.yaml
82 lines (69 loc) · 3.25 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
### Single 2-year activity query - compromise to cope with RAM. (no trendline)
generate_cohorts_bycode_emis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_EMIS_bycode
outputs:
highly_sensitive:
cohort: output/input_EMIS_bycode.csv
run_model_bycode_emis:
run: r:latest analysis/EMIS06-bycode.R
needs: [generate_cohorts_bycode_emis]
outputs:
moderately_sensitive:
log: logs/log-EMIS06-bycode.txt
#tb01: output/tables/EMISsc06_tb01_nat.csv
tb02: output/tables/EMISsc06_tb01_nat_red2.csv
fig03: output/plots/EMISsc06_fig03_pracnatcoverage.svg
### Monthly tallies.
generate_cohorts_long_emis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_EMISmeasures_bycode --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/emismeasures
outputs:
highly_sensitive:
cohort: output/emismeasures/input_EMISmeasures_bycode_*.csv
generate_measures_emis:
run: cohortextractor:latest generate_measures --study-definition study_definition_EMISmeasures_bycode --output-dir=output/emismeasures
needs: [generate_cohorts_long_emis]
outputs:
moderately_sensitive:
measure_csv: output/emismeasures/measure_*.csv
run_model_long_emis:
run: r:latest analysis/EMIS03-createnattrends_codes.R
needs: [generate_cohorts_long_emis]
outputs:
moderately_sensitive:
log: logs/log-EMIS03-createnattrends.txt
tb01: output/tables/EMISsc03_tb01_nattrends.csv
fig01: output/plots/EMISsc03_fig01_nattrends.svg
fig02: output/plots/EMISsc03_fig02_absnattrends.svg
fig03: output/plots/EMISsc03_fig03_pracnatcoverage.svg
run_model_measures_emis:
run: r:latest analysis/EMIS02-createtemporal.R
needs: [generate_cohorts_long_emis,generate_measures_emis]
outputs:
moderately_sensitive:
log: logs/log-EMIS02-createtemporal.txt
red_measures: output/tables/redacted_*.csv
figquant: output/plots/emisplot_quantiles_*_practice.svg
figlogquant: output/plots/emisplot_logquantiles_*_practice.svg
### Weekly tallies to compare with OC/VC supplier data. https://docs.opensafely.org/en/latest/measures/
generate_cohorts_weekly2021_emis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_EMISmeasures_weekly --index-date-range "2020-01-06 to 2021-05-31 by week" --output-dir=output/emismeasures-weekly
outputs:
highly_sensitive:
cohort: output/emismeasures-weekly/input_EMISmeasures_weekly_*.csv
generate_measures_weekly2021_emis:
run: cohortextractor:latest generate_measures --study-definition study_definition_EMISmeasures_weekly --output-dir=output/emismeasures-weekly
needs: [generate_cohorts_weekly2021_emis]
outputs:
moderately_sensitive:
measure_csv: output/emismeasures-weekly/measure_*.csv
run_model_weekly2021_emis:
run: r:latest analysis/EMIS04-weekly2021.R
needs: [generate_cohorts_weekly2021_emis,generate_measures_weekly2021_emis]
outputs:
moderately_sensitive:
log: logs/log-EMIS04-weekly2021.txt
tab1: output/tables/EMISsc04-weeklynattrend.csv